A project filter was '(project = ? OR scope = global)', which vec0 rejects in a nearest-neighbour query ('A LIMIT or k = ? constraint is required'). The only caller that passes a project is the de-duplication of new observations, which treats an error as 'insert', so semantic de-duplication never took effect.
Run one search for the project and one for global documents and merge them by distance without repeats, cut to the limit. QueryMultiField asks for enough field documents and keeps the best per observation; its two skipped tests are enabled. Because de-duplication now runs, canMergeInto skips a superseded or deleted note as a merge target.
Co-authored-by: Claude Sonnet 5.5 <[email protected]>
The vectors table is a vec0 virtual table, where INSERT OR REPLACE does not replace, so syncing a note that already had vectors failed with a UNIQUE constraint error and the edit never reached the index. AddDocuments also shadowed err inside its loop, so a failed insert left the write transaction open and later writes failed with 'database is locked'.
Add Client.ReplaceDocuments (delete and insert in one transaction) and use it from SyncObservation and SyncSummary. The shared write function has a named result, so every failed return rolls back. Fixes#66.
Co-authored-by: Claude Sonnet 5.5 <[email protected]>
MCP server (5 fixes):
- Move semaphore acquisition inside goroutine so main loop stays
responsive when all slots are taken
- Add 10s write timeout to sendResponse to prevent pipe deadlock
when Claude Code pauses reading stdout
- Send fallback JSON-RPC error when json.Marshal fails instead of
silently swallowing the error and leaving caller waiting forever
- Silence unknown notification methods (req.ID == nil) instead of
sending unsolicited error responses that may desync the host
- Return MCP isError content for tool failures instead of top-level
JSON-RPC error, matching the MCP specification
Vector/embedding (3 fixes):
- Move EmbedBatchWithContext call before writeMu.Lock in AddDocuments
so ONNX inference runs outside the write lock
- Replace singleflight.Do with DoChan + ctx select in both
getOrComputeEmbedding and UnifiedSearch so callers can bail out
independently when their context expires
- Add activeQueries atomic counter; skip cache warming when user
queries are in-flight; reduce warming timeout from 5s to 2s
Hooks (4 fixes):
- Cap EnsureWorkerRunning to 15s hard deadline with context; reduce
StartupTimeout from 30s to 10s; reduce port-in-use retries
- Fix nil dereference panic in user-prompt hook when initResult is
nil (non-JSON worker response); use comma-ok assertions
- Use package-level hookClient/healthClient with DisableKeepAlives
to prevent FD leaks in short-lived hook processes
- Set SysProcAttr{Setpgid: true} to detach worker from hook process
group, preventing kill-cascade from Claude Code
Worker/DB (3 fixes):
- Replace os.Exit(0) in MCP config watcher with context cancellation
for clean protocol shutdown
- Add 60s context.WithTimeout around ProcessObservation calls in
processAllSessions to prevent hung CLI subprocesses from blocking
the queue processor forever
- Set explicit PRAGMA wal_autocheckpoint=1000 and add PASSIVE WAL
checkpoint to Optimize() to prevent checkpoint stalls
Adds 20+ regression tests across all fix areas.
* Make things 'betterer' across the board
* fix: reorganize struct fields and config parameters for consistency
- [x] Reorder Config struct fields alphabetically and by related functionality
- [x] Reorganize Observation model fields with archival fields grouped together
- [x] Reorder ObservationStore fields to group related members
- [x] Reorder Store struct fields with health check caching grouped
- [x] Reorganize HealthInfo and PoolMetrics struct field order
- [x] Reorder maintenance Service struct fields logically
- [x] Reorganize MCP server handler parameter structs alphabetically
- [x] Reorder pattern detector candidate tracking fields
- [x] Reorganize search Manager struct fields by functionality
- [x] Reorder vector Client struct fields with mutex protections grouped
- [x] Reorganize handler request/response struct fields
- [x] Update handlers_test.go to expect wrapped response format
- [x] Reorder middleware TokenAuth and rate limiter fields
- [x] Reorganize Service struct fields with grouped functionality
- [x] Fix RateLimiter field ordering for clarity
- [x] Reorder CircuitBreaker metrics fields
* fix(security): improve JSON output safety and path traversal protection
- [x] Replace unsafe JSON string formatting with proper json.Marshal in export handler
- [x] Remove escapeJSONString helper function in favor of standard JSON marshaling
- [x] Add safeResolvePath function to validate paths and prevent directory traversal
- [x] Apply path traversal validation in captureFileMtimes operations
- [x] Cap result slice capacity in getRecentSearchQueries to prevent DoS via excessive allocation
* fix(sdk): improve path traversal protection and allocation safety
- [x] Enhance safeResolvePath with stricter validation using filepath.Rel
- [x] Reject paths containing ".." after cleaning to prevent traversal
- [x] Validate absolute paths are within cwd when cwd is specified
- [x] Apply safeResolvePath validation to GetFileContent for consistency
- [x] Add comprehensive test coverage for path traversal protection
- [x] Fix allocation safety in getRecentSearchQueries by using constant capacity
* feat(dashboard): add graph stats and vector metrics endpoints
- [x] Add handleGraphStats endpoint for knowledge graph visualization
- [x] Add handleVectorMetrics endpoint for vector database dashboard
- [x] Improve update check error handling with JSON response
- [x] Register new API routes for graph and vector metrics
- [x] Migrate Font Awesome to npm package from CDN
- [x] Fix observations API response type handling
- [x] Update package version to v0.10.5-15-g385d05a
* fixup! feat(dashboard): add graph stats and vector metrics endpoints
* test: add comprehensive test coverage across multiple packages
- [x] Add 298 tests for Python chunker functionality
- [x] Add 213 tests for chunking types and constants
- [x] Add 398 tests for TypeScript/JavaScript chunker
- [x] Add 954 tests for MCP server handlers and validation
- [x] Add 563 tests for pattern detector and analysis
- [x] Add 1149 tests for vector client cache and operations
- [x] Add 663 tests for SDK processor, circuit breaker, and deduplication
- [x] Add 731 tests for session manager lifecycle and concurrency
- [x] Add 331 tests for similarity clustering and term extraction
* fix(pattern): add nil check and fmt import for GetPatternInsight
- [x] Add `fmt` import for error formatting
- [x] Add nil check for pattern before using it
- [x] Remove duplicate comment line
* refactor(hooks): simplify hook execution with shared context
- [x] Extract BaseInput struct to eliminate duplicate fields across hooks
- [x] Create RunHook handler pattern for session-start and user-prompt
- [x] Create RunStatuslineHook for fast statusline rendering without worker startup
- [x] Add HookContext struct to pass port, project, CWD, SessionID to handlers
- [x] Add db/interface.go with ObservationReader/Writer interfaces
- [x] Add comprehensive conflict management tests in sqlite/conflict_test.go
- [x] Add vector client tests for Count, ModelVersion, NeedsRebuild, GetStaleVectors
- [x] Add FilterByThreshold helper tests for query result filtering
- [x] Make handlers_test more robust for network-dependent update checks
- [x] Update package versions in UI
* Move to GORM + general cleanup
* feat(mcp): add observation relations discovery and scoring integration
- [x] Add find_related_observations MCP tool for discovering related observations by confidence
- [x] Integrate scoring calculator and recalculator into MCP server initialization
- [x] Add pattern, relation, and session stores to MCP server dependencies
- [x] Register MCP server in Claude Code settings during plugin installation
- [x] Update install scripts (bash, PowerShell) to configure MCP server settings
- [x] Switch plugin manifest files to template-based versioning (plugin.json.tpl, marketplace.json.tpl)
- [x] Update all MCP server tests to pass new dependency parameters
* Resolves issue #13
- Switched model to bge-small-en-v1.5
- Added lazy re-embedding
- Added model version tracking per vector
- Added conversion of vectors to the new model
* Add lfs support to the workflow.
* Implements importance scoring with decay + voting #6
* Resolves issue #5 by marking observations as superseeded and scheduled for deletion
* Implement pattern detection #7
* Improve injections and observations accuracy
- Session start: Recent observations for project context (recency-based)
- User prompt: Semantically relevant observations (similarity-based with threshold)
* Added two stage retrieval with bi and cross encoder #8
* Implement query expansion and reformulation #9
* Knowledge graph and relationships ( resolves#4 )
- File Overlap Detection: Detects relationships when observations modify/read the same files
- Concept Overlap Detection: Detects relationships based on shared semantic concepts
- Type Progression Detection: Infers relationships from natural observation type progressions (e.g., discovery → bugfix = "fixes")
- Temporal Proximity Detection: Detects relationships between observations in the same session within 5 minutes
- Narrative Mention Detection: Detects explicit relationship language in narratives (e.g., "fixes", "depends on", "supersedes")
* Add visualisation of the relations to the dashboard.
* fixup! Add visualisation of the relations to the dashboard.
* Update documentation with new settings and screenshots.
lukaszraczylo